Washington: President Barack Obama will go ahead with his nomination of General John Allen to command NATO after he was cleared in a saga related to the sex scandal that felled CIA director David Petraeus, officials said.

"The investigation is now complete and General Allen's nomination to serve as the next Supreme Allied Commander Europe will proceed. We hope the Senate will consider it in a timely manner," White House spokesman Jay Carney said.

The Defence Department's inspector general exonerated Allen, currently the top general in Afghanistan, over emails sent to Florida socialite Jill Kelley, who threw parties for top brass at US Central Command.

The FBI came upon the emails from Allen in its probe of Petraeus, and defence officials had said the tone of the messages had been potentially "inappropriate" and possibly violated rules applying to military officers.

The scandal, over an affair with a biographer, prompted Petraeus to resign abruptly in November from his CIA post, ending a storied career marked by his tenure as military commander in the wars in Iraq and Afghanistan.

Initially, officials had said there were 25,000 to 30,000 pages of correspondence between Allen and Kelley, raising questions that his emails could reflect a distracted commander.

But officials later said the inquiry was only focused on a few hundred messages.

The scandal broke after Allen was nominated to take over as NATO's supreme allied commander, and his confirmation hearings before the US Senate were put on hold.